The Science and Applications of Microbial Genomics Workshop Summary (2013) / Chapter Skim
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Workshop Overview
Workshop Overview
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Nucleic acid sequencing technologies now provide access to the previously "unculturable" -- and thus, undetected -- microorganisms that comprise the majority of microbial life. Rapid and inexpensive sequencing platforms make it 1 The planning committee's role was limited to planning the workshop, and the workshop summary has been prepared by the workshop rapporteurs (with the assistance of Pamela Bertelson, Rebekah Hutton, and Katherine McClure)
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Using slight sequence differences between isolates to discriminate between closely related strains, investigators have tracked the evolution of isolates in a disease outbreak, traced person-to-person transmission of a communicable disease, and identified point sources of disease outbreaks. When genomic information about related strains or past disease outbreaks is available, the genome sequence of outbreak strains has proved useful in identifying factors that may contribute to the emergence, virulence, or spread of pathogens, as well as in speeding diagnostic tool development.
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Sections of the workshop summary not specifically attributed to an individual reflect the views of the rapporteurs and not those of the members of the Forum on Microbial Threats, its sponsors, or the IOM. The contents of the unattributed sections of this summary report provide a context for the reader to appreciate the presentations and discussions that occurred over the 2 days of this workshop.
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and evolution of life. One limitation is The fragments are then assembled into that each genome sequence is usually a larger pieces by looking for overlaps snapshot of one or a few individuals.
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The diversity of the microbial world is largely unknown, with less than one-half of 1% of the estimated 2–3 billion microbial species identified [emphasis added] ." Moreover, while there are well over 10 million species of "known" bacteria only a few thousand have been formally described (Eisen, 2007)
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1997. A Molecular View of Microbial Diversity and the Biosphere.
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Their work set a new course for the study and treatment of infectious disease-causing organisms. The "power and precision" of their studies
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THE CULTIVATION BOTTLENECK, GENOMICS, AND THE UNIVERSAL TREE OF LIFE In the 1950s and 1960s this focus on a few easily cultured organisms produced an explosion of information about microbial physiology and genetics that overshadowed efforts to understand the ecology and diversity of the microbial world (Pace, 1997)
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This had led some to characterize these species as the "weeds" of the microbial world (Hugenholtz, 2002)
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Initial molecular phylogeny studies demonstrated that this "unseen world" of microorganisms could be studied and confirmed that the number of organisms represented in the unculturable world far exceeded the size of the culturable world. While culture-based techniques remain the gold standard for disease detection, outbreak investigations, and infectious disease epidemiology, over the past several decades a range of sequence-based methods -- including broadrange PCR, high-throughput sequencing technologies, microarrays, and shotgun metagenomics -- have been applied to improve the detection and discovery of pathogens and other microorganisms.
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• Whole genome "resequencing" for the discovery of variants that differ in sequence to known genome sequences of a closely related strain. • Species classification and the identification of predicted coding sequences and novel gene discovery in genomic surveys of microbial communities (metagenomics)
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. Over the past several decades these advances have led to a proliferation of genome sequencing projects of bacteria, eukaryotes, and of entire microbial communities (metagenomes)
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. MICROBIOLOGY IN THE POST-GENOMIC ERA As of mid-2011, complete genome sequences had been published for 1,554 bacterial species (the majority of which are pathogens)
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Panel B shows the number of completed microbial genome sequences according to year (the most recent data were collected on April 21, 2011)
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These advances offer the hope that we can one day channel some of the activities of microorganisms for improvements to the health and well-being of plants, animals, humans, and ecosystems. USE OF WHOLE GENOME SEQUENCING IN OUTBREAK INVESTIGATIONS Recent examples, discussed below, of the use of whole genome sequencing to investigate outbreaks of emerging, reemerging, and novel infectious diseases
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When genomic information about related strains or past disease outbreaks is available, the genome sequence of outbreak strains has proved useful in identifying factors that may contribute to the emergence, virulence, or spread of pathogens, as well as in speeding diagnostic tool development. For example: • Investigators used genomic sequencing to investigate, and find the source for, the cholera outbreak in Haiti in 2010, a disease that had been absent from the island of Haiti for almost a century.
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Keim's contribution to the workshop summary report may be found in Appendix A, pages 207-229)
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2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.
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Study of the enzootic cycle is extremely difficult; however, sampling during an epizootic cycle or during human pandemics provides evidence for the changes occurring in the reservoir phase. FIGURE WO-8 Plague ecology.
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(2010) , who used whole genome sequencing and SNP typing to develop a phylogeny for Y
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2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.
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. Capitalizing on whole genome sequences and SNPs from U.S.
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Speaker Bruce Budowle of the University of North Texas Health Science Center defined microbial forensics as the analysis of evidence from an act of bioterrorism, biocrime, or inadvertent microorganism/toxin release for attribution purposes (Dr. Budowle's contribution to the workshop summary report may be found in Appendix A, pages 117-133)
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Again, the quality of sequence data and the results of bioinformatics analyses must be as high as possible. Budowle also emphasized the need for standard reference and test materials.
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Epidemiological investigation of Tracking endemic strains and identifying disease outbreaks; administrator of the sources of outbreak strains Select Agent Program NIAID Understanding disease mechanisms Research access to isolates for studies of (HHS-NIH) and host-pathogen interaction; pathogenicity mechanisms, host-pathogen development of treatments and response, and other R&D related to diagnostic assays medical countermeasures FDA (HHS)
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anthracis.17 At the same time, TIGR was in the final stages of assembling the first genome sequence of B anthracis and was asked to partner with the FBI and other laboratories to determine whether the complete genome sequence would be useful for purposes of attribution.
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Army Medical Research Institute of Infectious Diseases (USAMRIID) began to notice some B
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With current technologies investigators would be working with shorter sequence reads and, Fraser added, it is not possible to know if the gene duplication would have been as easy to identify from short reads as it was from the 800-plusbase-pair Sanger reads that were used at the time. What would community-level analysis with very deep coverage provide versus what was done by looking at single colonies?
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. Comparative analyses have revealed that the microbial genome is a dynamic entity shaped by multiple forces including gene loss/genome reduction, genome rearrangement, expansion of functional capabilities through gene duplication, and acquisition of functional capabilities through lateral or horizontal gene transfer, as shown in Figure WO-11 (Fraser-Liggett, 2005)
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In the case of B anthracis four genome sequences completely characterize the species (Medini et al., 2008)
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Multiple genome sequences are needed to describe the pan-genome, which represents, with the best approximation, the genetic information of a bacterial species. Metagenomics embraces the community as the unit of study and, in a specific environmental niche, defines the metagenome of the whole microbial population (d)
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Casadevall's contribution to the workshop summary report may be found in Appendix A, pages 134-140)
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Indeed, during the early 20th century, many common infectious diseases disappeared as a result of immunization, and microorganisms that were not previously considered pathogenic were increasingly associated with disease later in the century. The microbes did not change, noted Casadevall, "what happened was that we changed the host." Casadevall went on to emphasize that the concept of a "pathogen" is flawed, because it assumes that pathogenicity is an intrinsic, immutable characteristic of a microorganism.
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Host- vs. environment-acquired microbes The diversity of possible outcomes associated with many host–microbe interactions is also evident when one considers virulence factors associated with microbes acquired from another host or directly from the environment.
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neoformans. Applying a mathematical model to compute the relative contribution of microbial virulence factors, Casadevall estimated that the majority of cryptococcal virulence in mice 22 The environmentally acquired fungi Geomyces destructans and Batrachochytrium dendrobatidis, for example, currently pose a significant threat to populations of New World bats and amphibians worldwide (IOM, 2011)
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These insights have profound implications for detecting, diagnosing, and anticipating infectious disease emergence, including: • Bacterial genome sequence data have challenged the simplistic views that pathogens can be understood solely by identifying their virulence factors, and that pathogens often evolve from "nonpathogenic" organisms through the acquisition of virulence genes from plasmids, bacteriophages, or pathogenicity islands. Metagenomic surveys conducted in diverse en vironments have improved our understanding of the biodiversity and biogeography of microbes and have underscored the important role of environmental factors in disease emergence and spread.
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According to Rasko whole genome sequence analysis has rapidly advanced researchers' understanding of pathogenic variants of E coli -- an organism that has been intensely studied for almost 40 years.
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. Reprinted by permission from Macmillan Publishers Ltd: NATURE REVIEWS MICROBIOLOGY.
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. Rasko went on to observe that there is a mismatch between phylogeny based on the core genome, and phylotype based on virulence factors when characterizing which strains produce Shiga toxin (indicative of EHEC)
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40 FIGURE WO-15 Inconsistency of typing with whole genomes or MLST. SOURCE: Rasko (2012)
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coli isolates will have genes for components of the type III secretion system, while the presence of genes for other virulence factors (Shiga toxin 1 and 2, bundle-forming pilus) is extremely variable.
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Parkhill's contribution to the workshop summary report may be found in Appendix A, pages 257-269)
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SNPs are randomly distributed across the genome and exhibit a random rate for acquisition over time. Parkhill's group constructed a maximum likelihood phylogeny based on the 4,310 sites in the core genome of ST239 that contained one or more SNPs.
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44 FIGURE WO-17 Time dependence of dN/dS in the core and non-core genome. dN/dS ratio for 1,953 pairwise ST239 strain comparisons for the two sets of genes.
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Parkhill noted the use of homoplasy to identify selective pressures acting on isolates of other pathogenic bacteria, including Mycobacterium tuberculosis and Clostridium difficile. "By looking, not for dN/dS or all those classical measures of selection, but for things that don't fit the tree," Parkhill said, researchers can see selective pressures such as drug resistance and compensatory mutations, as well as evidence of selection on surface proteins, two-component sensor/regulators, and other genes that are likely to be under diversifying selection from host immune pressure.
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The El Tor strain of this pathogen is associated with the seventh cholera pandemic that originated in the early 1960s and persists today -- including the 2010 Haitian cholera outbreak. Before whole genome sequencing, cholera typing was done on the basis of the presence or absence, or variable sequences, of mobile elements.
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Transmission events inferred from the phylogenetic tree of the seventh pandemic lineage of V cholerae based on SNP differences across the whole core genome, excluding probable recombination events.
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Speaker Elodie Ghedin of the University of Pittsburgh School of Medicine elaborated on her interest in intra-host diversity, selection, and evolution of influenza viruses, which cause acute infections (Dr. Ghedin's contribution to the workshop summary report may be found in Appendix A, pages 151-165)
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This approach is illustrated in Figure WO-19, which depicts the alignment of short sequence reads from a sample to the gene sequence of interest -- in this case the neuraminidase gene sequence of influenza. Whereas consensus assembly would read the codon at position 275 as CAC (coding for histidine)
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Partial reconstruction of sequence reads into different viral genomes placed two variants into two phylogenetically distinct clades of the pandemic H1N1/2009 virus, a result that strongly suggests a mixed infection (Ghedin et al., 2011)
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Evolution of Novelty and Pathogenicity: Chytrid Fungal Pathogen of Amphibians Novel microbial pathogens do not just appear, they evolve, according to speaker Erica Bree Rosenblum of the University of California, Berkeley (Dr. Rosenblum's contribution to the workshop summary report may be found in Appendix A, pages 291-311)
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The absence of geographic or host-specific population structure confirms the rapid spread and broad host range of Bd. Yet the tree has more structure than expected, exhibiting two highly divergent lineages: a basal lineage with isolates from Latin America and a large clade with significant global diversity.
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. Rosenblum and colleagues compared the genomes of Bd and its closest relative, the nonpathogenic saprobe Homolaphlyctis polyrhiza, in order to investigate whether the protease gene family expansions accompanied the evolution of pathogenicity.
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Ritchie's contribution to the workshop summary report may be found in Appendix A, pages 269-290)
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Panel c, Functionally and taxonomically diverse microbial communities are found on the coral surface, within the gastrodermal cavity and in the intracellular spaces of the polyp. Coral-associated bacteria (B)
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and biofilm microbial communities facilitate attachment and settlement of coral larvae via inductive compounds (settlement cues) produced by the CCA or by recruiting specific bacteria that release these cues.
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Ritchie identified a number of antibiotic-producing bacterial species that were isolated from surface mucus that could contribute to this defense. Mucus collected during a bleaching event (i.e., when the coral were unhealthy or stressed)
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. The Human Microbiome Project, for example, seeks to map microbial communities associated with the different environments on and in the human body (e.g., gut, mouth, skin, vagina)
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. Reprinted by permission from Macmillan Publishers Ltd: NATURE.
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Comparisons of gene abundance may provide habitat-specific fingerprints that reflect known characteris tics of the sampled environment and "hint at certain nutrition conditions, novel genes, and systems contributing to a particular life style or environ mental interactions." Workshop speakers elaborated on several current metagenomics projects that seek to provide insights into the interactions among microorganisms within a community. Human-Associated Microbial Communities: Links to Health and Disease Just as microbes colonize the bobtail squid's light organ shortly after hatching, microbes colonize the human body internally and externally during its first weeks to years of life and become established in relatively stable communities in a variety of microhabitats (Dethlefsen et al., 2007)
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• tracking organisms (genetic variation in populations) Discovery of new bacterial taxa The Human Microbiome Project has generated a massive amount of 16S rRNA gene sequence data.31 16S rRNA differs for each bacterial species (Weinstock, 2012a)
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Further analysis of stool sample data from100 additional Human Microbiome Project participants demonstrated that most of the novel taxa were found in multiple individuals sampled at two different geographic locations (Wylie et al., 2012a)
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disease: Variation between communities A primary interest of the Human Microbiome Project is defining changes in a microbiome that are associated with disease. However, the intrinsic variation raises several important questions related to study design: • How does one approach hypothesis testing, and power and sample size determination?
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Species with a relative abundance > 0.35 percent are listed in order of relative abundance. As shown on the far-right column, species distribution from a metagenomic shotgun sequencing of pooled samples from normal individuals confirmed the high abundance of P
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acnes core genome. Only the topology is shown.
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Weinstock noted that investigators are just beginning to define different classes of communities within a body site; such as high and low bacterial communities of lactobacillus in the vagina. 34 A somewhat controversial area in human microbiome research, Weinstock said, is whether individuals or groups of people can be uniquely identified by their gut microbiomes.
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An analysis of nasal and plasma samples obtained from both febrile and afebrile children using shotgun FIGURE WO-28 Change in HIV communities with HAART. SOURCE: in collaboration with Homer Twigg of the Indiana University Medical School in Indianapolis (unpublished)
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Phylogenetic distribution and abundance of the 101 samples in the combined Human Microbiome Project-MetaHIT cohort were consistent with the usual community structure observed for the gut. By assessing the presence or absence of specific SNPs in samples collected from the same patient at different times, researchers have been able to show that strains present in an individual were fairly stable over time -- leading to the conclusion that a person has his or her own, unique, microbial communities that are distinct from the strains from another individual.
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Much of the fluid circulating through the crustal aquifer is discharged at deep-sea hydrothermal vents. These vents are prominent features along midocean ridges, and emit hot, chemically reduced fluids.
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is a slow and tedious process, and the nature, quality, and abundance of contextual data available to link specific microbes to biogeochemical processes varies widely. As such, there is an "impedance mismatch" between the volume and nature of data available from high-throughput sequencing technologies and the volume and nature of the contextual data obtained from geochemical sensors.
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. Pyrite in the system acts as a conductor and supports the establishment of a lush and diverse microbial community that is representative of what is seen in an active hydrothermal vent community freshly recovered from the sea floor (Schrenk et al., 2003; Takai et al., 2003)
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Community Ecology and Adaptation to the Environment -- Use of Genomic Approaches to Study Evolution in Real Time Comparative analyses of microbial genomes have demonstrated that the microbial genome is a dynamic entity shaped by multiple forces including gene loss/genome reduction, genome rearrangement, expansion of functional capabilities through gene duplication, and acquisition of functional capabilities through lateral or horizontal gene transfer (HGT) (Fraser-Liggett, 2005)
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. To study ecological differentiation in microbial communities, Alm sequenced Vibrionaceae strains from coastal bacterioplankton together with Martin Polz at the Massachusetts Institute of Technology (Hunt et al., 2008)
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2011. Ecology drives a global network of gene exchange connecting the human microbiome.
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Panel A, Phylogenetic tree of all strains, with outer and inner rings indicating seasons and size fractions of strain origin, respectively. Ecological populations predicted by the model are indicated by alternating blue and gray shading of clusters if they pass an empirical confidence threshold of 99.99 percent (see supporting online material for details)
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. Population genomics of early events in the ecological differentiationsof bacteria.
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Gilbert noted that unlike the Human Microbiome Project, the Earth Microbiome Project is not very well funded at the moment. Beyond funding, one of the biggest technical challenges is collecting samples from around the globe.
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it is possible to systematically catalog that community in a much more robust fashion. Sequences from the Earth Microbiome Project map to 82 percent of the Greengenes tree of life (compared to the Human Microbiome Project, which has thus far cataloged 17 percent of the tree)
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Gilbert went on to discuss several environment-specific microbiome projects under way, including the Home Microbiome Study that seeks to understand how humans interact with the microbes on their skin and the microbes in their home. We live in our spaces, but those spaces are also living, Gilbert said.
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PRACTICAL APPLICATIONS OF GENOMIC TECHNOLOGIES Applications of microbial genomics, such as those discussed throughout the workshop, have expanded researchers' appreciation for the biology of microorganisms including their organismal, metabolic, and environmental diversity; the structure of microbial populations over space and time; the evolution of microbial species; and the acquisition of novel virulence factors and pathogenicity islands. These areas of inquiry are providing important insights into the "ground rules" of
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ifferences in the sequence and structure of genomes from members of a microbial population reflect the composite effects of mutation, recombination, and selection. With the increasing availability of genome sequences, these effects have become better characterized and more effectively exploited in order to understand the history and evolution of microbes and viruses and their occasionally intimate relationships with humans.
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While we understand a great deal about the means of transmission for some pathogens -- measles and influenza viruses are spread on droplets, HIV is a blood-borne disease, and West Nile virus is a vector-borne viral disease -- public health epidemiologists do not yet fully understand how pathogens spread from person to person, from community to community, over space and time, and how underlying social network structures shape the movement of pathogens, said speaker Jennifer Gardy of the British Columbia Centre for Disease Control, Vancouver, Canada (Dr. Gardy's contribution to the workshop summary report may be found in Appendix A, pages 141-150)
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For the average bacterium, noted Gardy, MLST examines short fragments of seven housekeeping genes, essentially 0.03 percent of the available DNA. She continued, "that means you are ignoring 99.97 percent of its genome that contains informative and interesting variation that might give you a high-resolution view of an outbreak and that might actually be able to tell you about the order of transmission." The whole genome sequence has often been referred to in molecular epidemiology as "the ultimate genotype." With next-generation genome sequencing technology, molecular epidemiologists may be able to sequence numerous isolates from an outbreak quickly and cheaply.
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Gardy emphasized that in order to move forward with whole genome sequencing as a molecular epidemiology tool, it is important to remember that genomic data must be interpreted in the context of epidemiological and clinical data. It is not possible to reconstruct an outbreak from genome sequence alone.
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Gardy, et al., Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak, 364, 730-739. Copyright ©2011 Massachusetts Medical Society.
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Isolates from an outbreak in Birmingham Hospital, in 2008, were classified as indistinguishable by standard typing methods. Using whole genome sequencing of six isolates, Pallen's team was able to identify three loci that were SNP variations between isolates (Lewis et al., 2010)
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Pallen's collaborators in Hamburg sent DNA from an outbreak isolate to BGI42 for sequencing; BGI subsequently released the sequence data from five sequencing runs on the Ion Torrent platform into the public domain. Within 24 hours of release of the data, Nick Loman in Pallen's research group had assembled the genome and, through his blog post and Twitter account, called upon the bioinformatics community to analyze these data.
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Wang's contribution to the workshop summary report may be found in Appendix A, pages 311-338)
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An evaluation of the global diversity of viruses will provide researchers with important genomic libraries for future studies of novel viruses associated with disease outbreaks. Wang and colleagues are now evaluating more than 1,000 stool samples collected from patients with diarrhea or from healthy children, shared by collaborators from around the world.
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and did not respond to treatment with antibiotics. Multiple isolates appeared to be infected by viruses, and sequencing identified three novel viruses, one from a wild C
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Huse described analysis of the relative abundance of the microbiota in samples from the Human Microbiome Project (Huse et al., 2012)
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Rather than throwing these data away, Huse noted that researchers need better ways of finding singletons or rare organisms and seeing them in a context of other samples where they are not so rare. As Huse noted, there is no universal definition of "rare." For microorganisms, rare is not one or two, but tens of thousands, and even millions of cells.
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Meyer's contribution to the workshop summary report may be found in Appendix A, pages 230-238)
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MG-RAST requires the submission of metadata along with sequence data, and Meyer underscored the critical importance of metadata -- where the data are from, what procedures were used in data generation, and how the data were recorded -- to the interpretation of results. Meyer cited functional and taxonomic comparisons of 1,606 Human Microbiome Project shotgun metagenomes against 48 Kyoto Encyclopedia of Genes and Genomes.
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FIGURE WO-43 Principal coordinates analysis of 1,606 Human Microbiome Project shotgun metagenomes painted by sequencing technology. The purple dot is explained by a problem with the metadata and therefore should be green, but the metadata provided with the sample do not correctly identify it as Illumina (green)
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discard data sets or redo experiments." Predicting features Meyer described two basic methods for predicting protein coding features from genome sequence data: (1) statistics-based approaches using codon usage and (2)
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. The analysis bottleneck Computing costs of sequence analysis far outsize those associated with generating metagenomic sequencing data (Figure WO-44)
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. Each new platform has struck a different balance between cost, read length, data volume, and rate 50 Although the biochemistry of each platform is different, next-generation sequencing technologies feature simpler sample preparation steps, dispense with the need to create libraries of cloned sequences in bacteria, and rely on parallel, cyclic interrogation of sequences of clonal amplicons of DNA.
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Workshop speakers and participants discussed some of the key challenges in this rapidly advancing field, and potential methods to address them, focusing on the core themes of data quality and analysis. Comparability Across Sequencing Platforms and Technologies Perhaps the most formidable challenge for investigators using different sequencing technology platforms is data comparability across methods and FIGURE WO-45 Changes in instrument capacity over the past decade, and the timing of major sequencing projects.
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None of these sequencing platforms or assemblers gives perfect results. Training Gilbert observed that in addition to concordance between platforms, there are also issues of concordance within a platform.
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Louis, Missouri, is currently seeking CLIA approval. Data Quality: Careful Sample Preparation and Results Filtering Much of data quality resides in careful planning before sequencing, including primer design and sample preparation, and quality filtering of raw sequence reads before assembly and analysis -- approaches discussed earlier by Huse and Meyer.
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Pallen emphasized the importance of human involvement and the expertise of the microbiologist looking at the sequence data to make observations, find errors, and draw conclusions. Participants also discussed the importance of training in this regard as well as the performance of the sequencing platforms.
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As the amount of sequencing data continues to grow, consideration is needed of how to usefully record sequence data as well as experimental metadata. The Genomics Standards Consortium52 and the Sanger Institute have proposed standards for the description of genome sequences, including information about the origin, pathogenicity, host, growth conditions, estimated genome size, and 52 Thegenomic standards consortium is a consortium of groups, including the DNA Data Bank of Japan, the European Bioinformatics Institute, the European Molecular Biology Laboratory, the Joint Genome Institute, and the National Center for Biotechnology Information.
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As discussed earlier, it has become feasible for individual laboratories to undertake sequencing projects rather than sending samples to a few large genome centers. Current large-scale genome and metagenome sequencing projects are deploying multiple platforms and different sequencing chemistries in parallel.
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To aid the characterization of the human microbiota, for example, one of the goals of the human microbiome project is to sequence 3,000 bacterial genomes as a reference set, as well as other genomes from fungi and eukaryotic organisms (The Human Microbiome Jumpstart Reference Strains Consortium, 2010)
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. Looking Forward "Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science." -- Julian Davies, Professor Emeritus, Microbiology and Immunology, University of British Columbia In order to maximize the discovery and characterization of new gene families and their associated novel functions, Wu et al., (2009)
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Comparative genomic studies of bacterial species and metagenomic analyses of microbial communities to date have revealed how vastly we have underestimated the diversity, variability, and complexity of the microbial world. Microbial genomics offers the potential to efficiently characterize the vast cosmos of microbial diversity and rewrite the microbial community's tree of life.
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Paper presented at the Forum on Microbial Threats Workshop, The Science and Applications of Microbial Genomics, Wash ington, DC, Institute of Medicine, Forum on Microbial Threats, June 13. Casadevall, A., and L
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2002. The value of complete microbial genome sequencing (you get what you pay for)
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Paper pre sented at the Forum on Microbial Threats Workshop, The Science and Applications of Microbial Genomics, Washington, DC, Institute of Medicine, Forum on Microbial Threats, June 12. Hacker, J., and J
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. Paper presented at the Forum on Microbial Threats Workshop, The Science and Applications of Microbial Genomics, Washington, DC, Institute of Medicine, Forum on Microbial Threats, June 13.
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Nature Reviews Microbiology 10(9)
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2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.
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coli and Shigella: Identification and Charac terization of Pathogenic Variants Based on Whole Genome Sequence Analysis. Paper presented at the Forum on Microbial Threats Workshop, The Science and Applications of Microbial Ge nomics, Washington, DC, Institute of Medicine, Forum on Microbial Threats, June 12.
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2007. The human microbiome project.
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Paper presented at the Forum on Microbial Threats Workshop, The Science and Applications of Microbial Genomics, Washington, DC, Institute of Medicine, Forum on Microbial Threats, June 12. White, B
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